[med-svn] [Git][med-team/picard-tools][master] Fix Manifest

Steffen Möller gitlab at salsa.debian.org
Sat Sep 12 00:13:06 BST 2020 


Steffen Möller pushed to branch master at Debian Med / picard-tools


Commits:
5e179c29 by Steffen Moeller at 2020-09-12T01:12:01+02:00
Fix Manifest

- - - - -


4 changed files:

- debian/changelog
- debian/libpicard-java.manifest
- debian/patches/30-tests-fix-dataprovider.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+picard-tools (2.23.4+dfsg-2) unstable; urgency=medium
+
+  * Fixed classpath in picard.jar Manifest (s/:/ /g)
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 11 Sep 2020 23:40:02 +0200
+
 picard-tools (2.23.4+dfsg-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]


=====================================
debian/libpicard-java.manifest
=====================================
@@ -1,3 +1,3 @@
 usr/share/java/picard.jar:
   Main-Class: picard.cmdline.PicardCommandLine
-  Class-Path: /usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar
+  Class-Path: /usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/lib/jvm/default-java/lib/tools.jar /usr/share/java/commons-lang3.jar /usr/share/java/gkl.jar /usr/share/java/gatk-native-bindings.jar /usr/share/java/barclay.jar


=====================================
debian/patches/30-tests-fix-dataprovider.patch
=====================================
@@ -1,8 +1,10 @@
 Description: fix data provider requirements
 Author: Sascha Steinbiss <satta at debian.org>
+Index: picard-tools/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
+===================================================================
 --- picard-tools.orig/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
 +++ picard-tools/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
-@@ -31,33 +31,33 @@
+@@ -31,33 +31,33 @@ public class CollectHsMetricsTest extend
  
      @DataProvider(name = "collectHsMetricsDataProvider")
      public Object[][] targetedIntervalDataProvider() {
@@ -50,7 +52,7 @@ Author: Sascha Steinbiss <satta at debian.org>
          };
      }
  
-@@ -99,7 +99,7 @@
+@@ -99,7 +99,7 @@ public class CollectHsMetricsTest extend
                                          final long pfBases,
                                          final int sampleSize) throws IOException {
  
@@ -59,7 +61,7 @@ Author: Sascha Steinbiss <satta at debian.org>
          outfile.deleteOnExit();
  
          final String[] args = new String[] {
-@@ -141,14 +141,14 @@
+@@ -141,14 +141,14 @@ public class CollectHsMetricsTest extend
           *  Test that the depth histogram is [10,10,0,...,0]
           */
  
@@ -77,9 +79,11 @@ Author: Sascha Steinbiss <satta at debian.org>
          outfile.deleteOnExit();
  
          final String[] args = new String[] {
+Index: picard-tools/src/test/java/picard/util/IntervalListToolsTest.java
+===================================================================
 --- picard-tools.orig/src/test/java/picard/util/IntervalListToolsTest.java
 +++ picard-tools/src/test/java/picard/util/IntervalListToolsTest.java
-@@ -173,7 +173,6 @@
+@@ -173,7 +173,6 @@ public class IntervalListToolsTest exten
          };
      }
  
@@ -87,9 +91,11 @@ Author: Sascha Steinbiss <satta at debian.org>
      public void testActionsWithUnique(final IntervalListTools.Action action, final long bases, final int intervals) throws IOException {
          final IntervalList il = tester(action, false, true);
          Assert.assertEquals(il.getBaseCount(), bases, "unexpected number of bases found.");
+Index: picard-tools/src/test/java/picard/fingerprint/FingerprintCheckerTest.java
+===================================================================
 --- picard-tools.orig/src/test/java/picard/fingerprint/FingerprintCheckerTest.java
 +++ picard-tools/src/test/java/picard/fingerprint/FingerprintCheckerTest.java
-@@ -102,7 +102,6 @@
+@@ -102,7 +102,6 @@ public class FingerprintCheckerTest {
          };
      }
  
@@ -97,7 +103,7 @@ Author: Sascha Steinbiss <satta at debian.org>
      public void testCheckFingerprintsVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,
                                           final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) throws IOException {
          final Path indexedInputVcf = VcfTestUtils.createTemporaryIndexedVcfFromInput(vcfFile, "fingerprintcheckertest.tmp.").toPath();
-@@ -124,7 +123,6 @@
+@@ -124,7 +123,6 @@ public class FingerprintCheckerTest {
          Assert.assertEquals(mr.getLOD(), lodExpectedSample, DELTA);
      }
  
@@ -105,7 +111,7 @@ Author: Sascha Steinbiss <satta at debian.org>
      public void testFingerprintVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,
                                     final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) {
          final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);
-@@ -133,7 +131,6 @@
+@@ -133,7 +131,6 @@ public class FingerprintCheckerTest {
          Assert.assertFalse(fp1.isEmpty());
      }
  
@@ -113,16 +119,18 @@ Author: Sascha Steinbiss <satta at debian.org>
      public void testFingerprintSwapEqual(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,
                                           final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) {
          final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);
-@@ -476,4 +473,4 @@
+@@ -491,4 +488,4 @@ public class FingerprintCheckerTest {
  
          VcfTestUtils.assertVcfFilesAreEqual(vcfOutput, vcfExpected);
      }
 -}
 \ No newline at end of file
 +}
+Index: picard-tools/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java
+===================================================================
 --- picard-tools.orig/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java
 +++ picard-tools/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java
-@@ -21,13 +21,11 @@
+@@ -21,13 +21,11 @@ public class InfiniumDataFileTest {
          };
      }
  


=====================================
debian/rules
=====================================
@@ -18,6 +18,8 @@ override_dh_auto_build:
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	# ensure the .jar can be executed
+	/usr/bin/java -XX:ParallelGCThreads=1 -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -jar `find . -name "picard*.jar" BamIndexStats|head -n 1` -h > /dev/null
 	# Tests do not work with locales with a different decimal separator
 	# (for example ',')
 	env LC_ALL=C \



View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/5e179c294f3840f5f9c2edc282332af3f4aecfbe

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/5e179c294f3840f5f9c2edc282332af3f4aecfbe
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